Systematic sequencing of chloroplast transcript termini from Arabidopsis thaliana

Chloroplast transcription is highly promiscuous, requiring numerous steps to generate the ultimately complex but selective mixture of accumulating RNAs. To gain insight into how this RNA diversity is achieved and regulated, we focused on mapping transcript ends (the terminome) using Terminome-Seq, a protocol to systematically sequence RNA termini. Using Arabidopsis thaliana as a model, we generated a catalogue of >215 primary 5’ ends corresponding to transcription start sites (TSS), as well as 1,628 processed 5’ ends and 1,299 3’ ends.